In 2009, two days after taking office, President Barack Obama in Executive Order 13491 repudiated and revoked all legal guidance on interrogation authored by Yoo and his successors in the Office of Legal Counsel between September 11, 2001, and January 20, 2009.[5][6] At the time of the Obama administration, he continues to be a Professor of Law at the University of California, Berkeley.

Yoo's legal opinions were not shared by everyone within the Bush Administration. Secretary of State Colin Powell strongly opposed what he saw as an invalidation of the Geneva Conventions,[16] while U.S. Navy general counsel Alberto Mora campaigned internally against what he saw as the "catastrophically poor legal reasoning" and dangerous extremism of Yoo's opinions.[17]

In December 2003, Yoo's memo on permissible interrogation techniques, also known as the Bybee memo, was repudiated as legally unsound by the OLC, then under the direction of Jack Goldsmith.[17] In June 2004, another of Yoo's memos on interrogation techniques was leaked to the press, after which it was repudiated by Goldsmith and the OLC.[18]

Yoo's contribution to these memos has remained a source of controversy following his departure from the Justice Department;[19] he was called to testify before the House Judiciary Committee in 2008 in defense of his role.[20] The Justice Department's Office of Professional Responsibility (OPR) began investigating Yoo's work in 2004 and in July 2009 completed a report that was sharply critical of his legal justification for waterboarding and other interrogation techniques.[21][22][23][24] The OPR report cites testimony Yoo gave to Justice Department investigators in which he claims that the "president's war-making authority was so broad that he had the constitutional power to order a village to be 'massacred'"[25] The OPR report concluded that Yoo had "committed 'intentional professional misconduct' when he advised the CIA it could proceed with waterboarding and other aggressive interrogation techniques against Al Qaeda suspects", although the recommendation that he be referred to his state bar association for possible disciplinary proceedings was overruled by David Margolis, another senior Justice department lawyer.[25]

After he left the Department of Justice, it was revealed that Yoo had written legal opinions, including co-writing the Torture Memo of August 1, 2002, that narrowly defined torture and American habeas corpus obligations. They authorized what were called enhanced interrogation techniques and were issued to the CIA.[26][27][28] In addition, at the time the OLC issued a new definition of torture. Most actions that fall under the international definition did not fall within this new definition advocated by the U.S.[29]

In addition, on March 14, 2003, Yoo wrote a legal opinion memo in response to the General Counsel of the Department of Defense, in which he concluded that torture not allowed by federal law could be used by interrogators in overseas areas.[30]

In 2004 Jack Goldsmith, then head of the OLC, advised agencies not to rely on these memos and withdrew them as authorized legal opinions.

Several top military lawyers, including Alberto J. Mora, reported that policies allowing methods equivalent to torture were developed in the highest levels of the administration. Lawyers within the Department of Defense worked internally to circumvent those policies and instead mandate non-coercive interrogation standards, but were not successful.[31][32]

On December 1, 2005, Yoo appeared in a debate in Chicago with Doug Cassel, a law professor from the University of Notre Dame. During the debate, Cassel asked Yoo,

"If the President deems that he's got to torture somebody, including by crushing the testicles of the person's child, there is no law that can stop him?", to which Yoo replied "No treaty." Cassel followed up with "Also no law by Congress—that is what you wrote in the August 2002 memo", to which Yoo replied "I think it depends on why the President thinks he needs to do that."[33]

On June 26, 2008, Yoo and David Addington, former counsel and chief of staff to Vice-President Dick Cheney, testified before the House Judiciary Committee in what became a contentious hearing on detainee treatment, interrogation methods, and the extent of executive branch authority.[20][34][35][36]

Yoo also authored the October 23, 2001 memo asserting that the President had sufficient power to allow the NSA to monitor the communications of US citizens on US soil without a warrant (known as the warrantless wiretap program) because the Fourth Amendment does not apply. Or, as another memo says in a footnote, "Our office recently concluded that the Fourth Amendment had no application to domestic military operations." [37][38]

In a 2006 book and a 2007 law review article, Yoo defended President Bush's terrorist surveillance program, arguing that "the TSP represents a valid exercise of the President's Commander-in-Chief authority to gather intelligence during wartime".[39] He claimed that critics of the program misunderstand the separation of powers between the President and Congress in wartime because of a failure to understand the differences between war and crime, and a difficulty in understanding the new challenges presented by a networked, dynamic enemy such as Al Qaeda. "Because the United States is at war with Al Qaeda, the President possesses the constitutional authority as Commander-in-Chief to engage in warrantless surveillance of enemy activity."[39] In a Wall Street Journal opinion piece in July 2009, Yoo wrote it was "absurd to think that a law like FISA should restrict live military operations against potential attacks on the United States."[40]

Yoo suggested that since the primary task of the President during a time of war is protecting U.S. citizens, the President has inherent authority to subordinate independent government agencies, and plenary power to use force abroad.[41] Yoo contends that the Congressional check on Presidential war-making power comes from its power of the purse. He says that the President, and not the Congress or courts, has sole authority to interpret international treaties such as the Geneva Conventions "because treaty interpretation is a key feature of the conduct of foreign affairs".[42] His positions on executive power are controversial because the theory can be interpreted as holding that the President's war powers afford him executive privileges which exceed the bounds which other scholars associate with the President's war powers.[42][43][44][45]

In 1998 Yoo criticized what he characterized as an imperial use of executive power by the Clinton administration.[46] Yoo has defended executive privilege, but only to protect national security, diplomatic, and military secrets. In an opinion piece in the WSJ, he criticized the Clinton administration for misusing the privilege to protect the personal, rather than official, activities of the President, such as in the Monica Lewinsky affair.[47]At the time, Yoo also criticized President Clinton for contemplating defiance of a judicial order. He suggested that Presidents could act in conflict with the Supreme Court, but that such measures were justified only during emergencies.[48]

In 2000 Yoo strongly criticized what he viewed as the Clinton administration's use of powers of what he termed the "Imperial Presidency". He said it undermined "democratic accountability and respect for the law".[49] Yet, Yoo has defended President Clinton, for his decision to use force abroad without congressional authorization. He wrote in the Wall Street Journal on March 15, 1999, that Clinton's decision to attack Serbia was constitutional. He then criticized Democrats in Congress for not suing Clinton as they had sued presidents Bush and Reagan to stop the use of force abroad. [50]

Following his tenure as an appointee of the George W. Bush Administration, Yoo criticized certain views on the separation of powers doctrine as allegedly being historically inaccurate and problematic for the global war on terrorism. For instance, he wrote,

We are used to a peacetime system in which Congress enacts the laws, the president enforces them, and the courts interpret them. In wartime, the gravity shifts to the executive branch.[51]

and

To his critics, Mr. Bush is a 'King George' bent on an "imperial presidency". But the inescapable fact is that war shifts power to the branch most responsible for its waging: the executive.[52]

the possibility that the authors of these memoranda counseled the use of lethal and unlawful techniques, and therefore face criminal culpability themselves. That, after all, is the teaching of United States v. Altstötter, the Nuremberg case brought against German Justice Department lawyers whose memoranda crafted the basis for implementation of the infamous 'Night and Fog Decree'.[28]

Legal scholars speculated shortly thereafter that the case has little chance of successfully making it through the German court system.[57]

Jordan Paust of the University of Houston Law Center concurred with supporters of prosecution and in early 2008 criticized the US Attorney General Michael Mukasey's refusal to investigate and/or prosecute anyone who relied on these legal opinions:

[I]t is legally and morally impossible for any member of the executive branch to be acting lawfully or within the scope of his or her authority while following OLC opinions that are manifestly inconsistent with or violative of the law. General Mukasey, just following orders is no defense![58]

On April 13, 2013, the Russian Federation banned Yoo and several others from entering the country because of alleged human rights violations. The list was a direct response to the so-called Magnitsky list revealed by the United States the day before.[60][61] Russia stated that Yoo was among those responsible for “the legalization of torture” and “unlimited detention”.[62][63]

On January 4, 2008, José Padilla, a U.S. citizen convicted of terrorism, and his mother sued John Yoo in the U.S. District Court, Northern District of California (Case Number 08-cv-00035-JSW), known as Padilla v. Yoo.[65] The complaint sought $1 in damages based on the alleged torture of Padilla, attributed to the authorization by Yoo's torture memoranda. Judge Jeffrey S. White allowed the suit to proceed, rejecting all but one of Yoo's immunity claims. Padilla's lawyer says White's ruling could have a broad effect for all detainees.[66][67][68]

Soon after his appointment in October 2003 as chief of the Office of Legal Counsel, DOJ, Jack Goldsmith withdrew Yoo's torture memoranda. The Padilla complaint, on page 20, cited Goldsmith's 2007 book The Terror Presidency in support of its case. In it Goldsmith had claimed that the legal analysis in Yoo's torture memoranda was incorrect and that there was widespread opposition to the memoranda among some lawyers in the Justice Department. Padilla's attorney used this information in the lawsuit, saying that Yoo caused Padilla's damages by authorizing his alleged torture by his memoranda.[69][70]

While the District Court ruled in favor of Padilla, the case was appealed by Yoo in June 2010. On May 2, 2012, the Ninth Circuit Court of Appeals held that Yoo had qualified immunity at the time of his memos (2001–2003), because certain issues had not then been settled legally by the U.S. Supreme Court. Based on the Supreme Court's decision in Ashcroft v. al-Kidd (2011), the Appeals Court unanimously ruled against Padilla, saying that, when he was held as a detainee, it had not been established that an enemy combatant had the "same constitutional protections" as a convicted prisoner or suspect, and that his treatment had not been legally established at the time as torture.[71]

Haynes, Feith, Yoo, Bybee, Gonzales and—at the apex—Addington, should never travel outside the US, except perhaps to Saudi Arabia and Israel. They broke the law; they violated their professional ethical code. In the future, some government may build the case necessary to prosecute them in a foreign court, or in an international court.[72]

The Department of Justice's Office of Professional Responsibility concluded in a 261-page report dated July 29, 2009, that Yoo committed "intentional professional misconduct" when he "knowingly failed to provide a thorough, objective, and candid interpretation of the law", and it recommended a referral to the Pennsylvania Bar for disciplinary action.[73] But, David Margolis, a career Justice attorney,[74] in a Memorandum dated January 5, 2010, countermanded the recommended referral.[75] While Margolis was careful to avoid "an endorsement of the legal work," which he said was "flawed" and "contained errors more than minor", concluding that Yoo had exercised "poor judgment", he did not find "professional misconduct" sufficient to authorize OPR "to refer its findings to the state bar disciplinary authorities".[75]

Yoo contended that the OPR had shown "rank bias and sheer incompetence", intended to "smear my reputation", and that Margolis "completely rejected its recommendations".[76]

Although stopping short of referral to the bar, Margolis had also written:

[Yoo's and Bybee's] memoranda represent an unfortunate chapter in the history of the Office of Legal Counsel. While I have declined to adopt OPR's findings of misconduct, I fear that John Yoo's loyalty to his own ideology and convictions clouded his view of his obligation to his client and led him to author opinions which reflected his own extreme, although sincerely held, views of executive power while speaking for an institutional client.[75]

Yoo's writings and areas of interest have fallen into three broad areas: American foreign relations; the Constitution's separation of powers and federalism; and international law. In foreign relations, Yoo has argued that the original understanding of the Constitution gives the President the authority to use armed force abroad without congressional authorization, subject to Congress's power of the purse; that treaties do not generally have domestic legal force without implementing legislation; and that courts are functionally ill-suited to intervene in foreign policy disputes between the President and Congress.

With the separation of powers, Yoo has argued that each branch of government has the authority to interpret the Constitution for itself, which provides the justification for judicial review by the federal courts.[citation needed] In international law, Yoo has written that the rules governing the use of force must be understood to allow nations to engage in armed intervention to end humanitarian disasters, rebuild failed states, and stop terrorism and the proliferation of weapons of mass destruction.[77][78][79][80][81]

During 2012 and 2014, Yoo published two books with Oxford University Press. Taming Globalization was co-authored with Julian Ku in 2012, and Point of Attack was published under his single authorship in 2014.

^Yoo, John (January 19, 2008). "Opinion: Terrorist Tort Travesty". The Wall Street Journal. p. A13. Retrieved 2008-02-10. Last week, I (a former Bush administration official) was sued by José Padilla—a 37-year-old al Qaeda operative convicted last summer of setting up a terrorist cell in Miami. Padilla wants a declaration that his detention by the U.S. government was unconstitutional, $1 in damages, and all of the fees charged by his own attorneys.